Abstract
Caligus rogercresseyi, commonly known as sea louse, is an ectoparasite copepod that impacts the salmon aquaculture in Chile, causing losses of hundreds of million dollars per year. In this study, we report a chromosome-scale assembly of the sea louse (C. rogercresseyi) genome based on single-molecule real-time sequencing (SMRT) and proximity ligation (Hi-C) analysis. Coding RNAs and non-coding RNAs, and specifically long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) were identified through whole transcriptome sequencing from different life stages. A total of 23,686 protein-coding genes and 12,558 non-coding RNAs were annotated. In addition, 6,308 lncRNAs and 5,774 miRNAs were found to be transcriptionally active from larvae to adult stages. Taken together, this genomic resource for C. rogercresseyi represents a valuable tool to develop sustainable control strategies in the salmon aquaculture industry.
Highlights
Background & SummarySea lice are marine copepods that negatively impact the salmon aquaculture worldwide
Lice spend a large part of their life cycle on a fish host, displaying specific mechanisms for evading the host’s immune response[9,10,11]
Adult female specimens of Caligus rogercresseyi were collected from Atlantic salmon (Salmo salar) at the Caligus Reference Laboratory (CRL), University of Concepción, Chile (Fig. 1)
Summary
Background & SummarySea lice are marine copepods that negatively impact the salmon aquaculture worldwide. Short-read sequencing libraries were prepared using an insert size of 150 bp obtained from 1 μg of genomic DNA, after fragmentation, end-paired, and ligation to adaptors, respectively. These long subreads were assembled with the Canu V1.5 package[32] using default parameters, yielding a draft genome for the sea louse equivalent to 727 Mb with contig N50 of 43,366 bp and 35.55 GC%.
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